[ccp4bb]: Averaging structures using optimize_average.inp

[Tristan Fiedler <tfiedler@newssun.med.miami.edu>]

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I am dealing with the same issue that was posted to the CCP4BB about a
year ago :

> [ccp4bb]: How to average coordinates?
> 
> 
> 
>      To: "ccp4bb@dl.ac.uk" <ccp4bb@dl.ac.uk> 
>      Subject: [ccp4bb]: How to average coordinates? 
>      From: diane h peapus <dp72@cornell.edu> 
>      Date: Thu, 22 Feb 2001 21:53:51 -0500 
>      Sender: owner-ccp4bb@dl.ac.uk 
> 
> 
> 
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> ***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***
> 
> 
> Hi All:
> 
> I'm looking for a program that can average several .pdb files
> to give the average structure.  I got these .pdb files from
> several different anneal runs using CNS.  I then ran CNS's
> optimize_average.inp, which says that it...
> "Finds optimum combination of coordinate files which produce
> minimum free R-value from averaged structure factors."
> 
> This tells me which of my .pdb files to average to get the
> best Rfree... but doesn't output a .pdb file with the
> averaged structures.   hummm...
> 
> So, can anyone tell me a program that I can average my
> structures, now that I know which will give the best Rfree?


No follow-up answers were posted to the CCP4BB, nor does anything useful
come from a web search.

In order to use the best 4 structures (out of 10) listed in the end of
the (CNS) optimize_average.list  file to obtain an SA omit map, should a
single composite PDB be constructed (as suggested in the above posting)
or should the best 4 (in this case) structures be input to CNS
composite_omit_map.inp ?

Thank you for any suggestions,

tristan


-- 
Tristan J. Fiedler, Ph.D.
Malhotra Laboratory
Department of Biochemistry & Molecular Biology
University of Miami Medical School

t.fiedler@umiami.edu
tfiedler@newssun.med.miami.edu